RAM for genome index with STAR
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5 months ago
Fizzah ▴ 20

Hello there, I am trying to index Gossypium hirsutum reference genome with STAR but the command stays for 2 days at " starting to sort Suffix Array. This may take a long time...". later I found out this problem is due to RAM allocation. I have 32 GB RAM in total.

1.Please address this issue and tell me how much RAM allocation would be enough for STAR indexing.

  1. How can I allocate RAM by giving parameters in the command given below

Note: this the command I used

STAR --runMode genomeGenerate --genomeDir indexes/Gh \
            --genomeFastaFiles /home/pg/Fizzah/reference_genome/genome_assemblies_genome.fasta/ncbi-genomes-2021-12-15/GCF_007990345.1_Gossypium_hirsutum_v2.1_genomic.fna \
            --sjdbGTFfile /home/pg/Fizzah/reference_genome/genome_assemblies_genome.gtf/ncbi-genomes-2021-12-15/GCF_007990345.1_Gossypium_hirsutum_v2.1_genomic.gtf \
            --sjdbOverhang 149 --outFileNamePrefix Gh_RefIndex
STAR Indexing RAM • 423 views
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Have you tried --runThreadN? Ref

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Please share your additional information that has lead you to conclude that this issue is due to RAM allocation.

a previous Biostars post has addressed a similar issue STAR genome generate memory requirements looks like the issue was the input file that was being specified but other answers suggest setting the --limitGenomeGenerateRAM parameter

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also depending on how large the G. hirsutum genome is, 32 GB may not be enough memory

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